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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
75 lines
2.1 KiB
YAML
75 lines
2.1 KiB
YAML
name: bbmap_bbsplit
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description: write your description here
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keywords:
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- align
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- map
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- genome
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- reference
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tools:
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- bbmap:
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description: BBMap is a short read aligner, as well as various other bioinformatic tools.
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homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
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documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
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tool_dev_url: None
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doi: ""
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licence: ["UC-LBL license (see package)"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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- index:
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type: directory
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description: Directory to place generated index
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pattern: "*"
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- primary_ref:
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type: path
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description: Path to the primary reference
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pattern: "*"
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- other_ref_names:
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type: list
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description: List of other reference ids apart from the primary
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- other_ref_paths:
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type: list
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description: Path to other references paths corresponding to "other_ref_names"
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- only_build_index:
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type: string
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description: true = only build index; false = mapping
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- index:
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type: directory
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description: Directory with index files
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pattern: "bbsplit"
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- primary_fastq:
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type: file
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description: Output reads that map to the primary reference
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pattern: "*primary*fastq.gz"
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- all_fastq:
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type: file
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description: All reads mapping to any of the references
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pattern: "*fastq.gz"
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- stats:
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type: file
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description: Tab-delimited text file containing mapping statistics
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pattern: "*.txt"
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authors:
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- "@joseespinosa"
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- "@drpatelh"
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